Phenotype#
lamindb provides access to the following public protein ontologies through lnschema-bionty:
Here we show how to access and search phenotype ontologies to standardize new data.
Setup#
!lamin init --storage ./test-phenotype --schema bionty
✅ saved: User(uid='DzTjkKse', handle='testuser1', name='Test User1', updated_at=2024-01-08 10:59:25 UTC)
✅ saved: Storage(uid='DempsgrC', root='/home/runner/work/lamin-usecases/lamin-usecases/docs/test-phenotype', type='local', updated_at=2024-01-08 10:59:25 UTC, created_by_id=1)
💡 loaded instance: testuser1/test-phenotype
💡 did not register local instance on hub
import lnschema_bionty as lb
import pandas as pd
Bionty objects#
Let us create a public knowledge accessor with bionty(), which chooses a default public knowledge source from BiontySource. It’s a Bionty object, which you can think about as a less-capable registry:
phenotype_bt = lb.Phenotype.bionty()
phenotype_bt
💡 loaded instance: testuser1/test-phenotype
Phenotype
Organism: human
Source: hp, 2023-06-17
#terms: 17653
📖 Phenotype.df(): ontology reference table
🔎 Phenotype.lookup(): autocompletion of terms
🎯 Phenotype.search(): free text search of terms
✅ Phenotype.validate(): strictly validate values
🧐 Phenotype.inspect(): full inspection of values
👽 Phenotype.standardize(): convert to standardized names
🪜 Phenotype.diff(): difference between two versions
🔗 Phenotype.ontology: Pronto.Ontology object
As for registries, you can export the ontology as a DataFrame:
df = phenotype_bt.df()
df.head()
| name | definition | synonyms | parents | |
|---|---|---|---|---|
| ontology_id | ||||
| HP:0000001 | All | None | None | [] |
| HP:0000002 | Abnormality of body height | Deviation From The Norm Of Height With Respect... | Abnormality of body height | [HP:0001507] |
| HP:0000003 | Multicystic kidney dysplasia | Multicystic Dysplasia Of The Kidney Is Charact... | Multicystic dysplastic kidney|Multicystic rena... | [HP:0000107] |
| HP:0000005 | Mode of inheritance | The Pattern In Which A Particular Genetic Trai... | Inheritance | [HP:0000001] |
| HP:0000006 | Autosomal dominant inheritance | A Mode Of Inheritance That Is Observed For Tra... | Autosomal dominant|monoallelic_autosomal | [HP:0034345] |
Unlike registries, you can also export it as a Pronto object via phenotype_bt.ontology.
Look up terms#
As for registries, terms can be looked up with auto-complete:
lookup = phenotype_bt.lookup()
The . accessor provides normalized terms (lower case, only contains alphanumeric characters and underscores):
lookup.eeg_with_persistent_abnormal_rhythmic_activity
Phenotype(ontology_id='HP:0010846', name='EEG with persistent abnormal rhythmic activity', definition=None, synonyms='EEG: persistent abnormal rhythmic activity', parents=array(['HP:0011176'], dtype=object))
To look up the exact original strings, convert the lookup object to dict and use the [] accessor:
lookup_dict = lookup.dict()
lookup_dict["EEG with persistent abnormal rhythmic activity"]
Phenotype(ontology_id='HP:0010846', name='EEG with persistent abnormal rhythmic activity', definition=None, synonyms='EEG: persistent abnormal rhythmic activity', parents=array(['HP:0011176'], dtype=object))
By default, the name field is used to generate lookup keys. You can specify another field to look up:
lookup = phenotype_bt.lookup(phenotype_bt.ontology_id)
lookup.hp_0000003
Phenotype(ontology_id='HP:0000003', name='Multicystic kidney dysplasia', definition='Multicystic Dysplasia Of The Kidney Is Characterized By Multiple Cysts Of Varying Size In The Kidney And The Absence Of A Normal Pelvicaliceal System. The Condition Is Associated With Ureteral Or Ureteropelvic Atresia, And The Affected Kidney Is Nonfunctional.', synonyms='Multicystic dysplastic kidney|Multicystic renal dysplasia|Multicystic kidneys', parents=array(['HP:0000107'], dtype=object))
Search terms#
Search behaves in the same way as it does for registries:
phenotype_bt.search("dysplasia").head(3)
| ontology_id | definition | synonyms | parents | __ratio__ | |
|---|---|---|---|---|---|
| name | |||||
| Hip dysplasia | HP:0001385 | The Presence Of Developmental Dysplasia Of The... | Congenital hip dysplasia | [HP:0003272] | 95.0 |
| Superior cerebellar dysplasia | HP:0020185 | Abnormal Morphological Development Of The Supe... | None | [HP:0007033] | 90.0 |
| Dysplastic tricuspid valve | HP:0030732 | A Congenital Malformation Of The Tricuspid Val... | Tricuspid valve dysplasia | [HP:0001702] | 90.0 |
By default, search also covers synonyms:
phenotype_bt.search("Congenital hip dysplasia").head(3)
| ontology_id | definition | synonyms | parents | __ratio__ | |
|---|---|---|---|---|---|
| name | |||||
| Hip dysplasia | HP:0001385 | The Presence Of Developmental Dysplasia Of The... | Congenital hip dysplasia | [HP:0003272] | 100.000000 |
| Congenital hip dislocation | HP:0001374 | None | Congenital hip dislocations|Dislocated hip sin... | [HP:0002827] | 80.000000 |
| Congenital alveolar dysplasia | HP:0033210 | Arrest Of Lung Development In The Cananicular ... | None | [HP:0006703] | 79.245283 |
Search another field (default is .name):
phenotype_bt.search(
"lack of development of speech and language", field=phenotype_bt.definition
).head()
| ontology_id | name | synonyms | parents | __ratio__ | |
|---|---|---|---|---|---|
| definition | |||||
| Complete Lack Of Development Of Speech And Language Abilities. | HP:0001344 | Absent speech | Lack of speech|Absent speech development|Lack ... | [HP:0000750, HP:0002167] | 81.553398 |
| Lack Of Development Of One Lung. | HP:0030707 | Unilateral lung agenesis | Unilateral pulmonary agenesis | [HP:0006703] | 76.712329 |
| Absence Of The Nasal Bone. | HP:0010941 | Aplasia of the nasal bone | Lack of development of the nasal bone|Failure ... | [HP:0010940] | 73.417722 |
| Agenesis Of Canine Tooth. | HP:0012738 | Agenesis of canine | Failure of development of canine|Failure of de... | [HP:0001592, HP:0011078] | 67.567568 |
| Agenesis Of Secondary Molar Tooth. | HP:0011055 | Agenesis of permanent molar | Failure of development of permanent molar|Agen... | [HP:0011054] | 67.469880 |
Standardize phenotype identifiers#
Let us generate a DataFrame that stores a number of phenotype identifiers, some of which corrupted:
df_orig = pd.DataFrame(
index=[
"Specific learning disability",
"Dystonia",
"Cerebral hemorrhage",
"Slurred speech",
"This phenotype does not exist",
]
)
df_orig
| Specific learning disability |
|---|
| Dystonia |
| Cerebral hemorrhage |
| Slurred speech |
| This phenotype does not exist |
We can check whether any of our values are validated against the ontology reference:
validated = phenotype_bt.validate(df_orig.index, phenotype_bt.name)
df_orig.index[~validated]
✅ 4 terms (80.00%) are validated
❗ 1 term (20.00%) is not validated: This phenotype does not exist
Index(['This phenotype does not exist'], dtype='object')
Ontology source versions#
For any given entity, we can choose from a number of versions:
lb.BiontySource.filter(entity="Phenotype").df()
| uid | entity | organism | currently_used | source | source_name | version | url | md5 | source_website | created_at | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||
| 37 | 3SSF | Phenotype | human | True | hp | Human Phenotype Ontology | 2023-06-17 | https://github.com/obophenotype/human-phenotyp... | 65e8d96bc81deb893163927063b10c06 | https://hpo.jax.org | 2024-01-08 10:59:25.504655+00:00 | 2024-01-08 10:59:25.504664+00:00 | 1 |
| 38 | tC5E | Phenotype | human | False | hp | Human Phenotype Ontology | 2023-04-05 | https://github.com/obophenotype/human-phenotyp... | bdf866e11d37cf6fd2aef25c325b2c8a | https://hpo.jax.org | 2024-01-08 10:59:25.504754+00:00 | 2024-01-08 10:59:25.504763+00:00 | 1 |
| 39 | q03N | Phenotype | human | False | hp | Human Phenotype Ontology | 2023-01-27 | https://github.com/obophenotype/human-phenotyp... | ceeb3ada771908deef620d74cd8e6b0f | https://hpo.jax.org | 2024-01-08 10:59:25.504854+00:00 | 2024-01-08 10:59:25.504863+00:00 | 1 |
| 40 | nwdt | Phenotype | mammalian | True | mp | Mammalian Phenotype Ontology | 2023-05-31 | https://github.com/mgijax/mammalian-phenotype-... | be89052cf6d9c0b6197038fe347ef293 | https://github.com/mgijax/mammalian-phenotype-... | 2024-01-08 10:59:25.504955+00:00 | 2024-01-08 10:59:25.504964+00:00 | 1 |
| 41 | zAfB | Phenotype | zebrafish | True | zp | Zebrafish Phenotype Ontology | 2022-12-17 | https://github.com/obophenotype/zebrafish-phen... | 03430b567bf153216c0fa4c3440b3b24 | https://github.com/obophenotype/zebrafish-phen... | 2024-01-08 10:59:25.505071+00:00 | 2024-01-08 10:59:25.505083+00:00 | 1 |
| 42 | soFx | Phenotype | human | False | phe | Phecodes ICD10 map | 1.2 | s3://bionty-assets/df_human__phe__1.2__Phenoty... | 741033ee1b13df7c41b4849e8bd02f13 | https://phewascatalog.org/phecodes_icd10 | 2024-01-08 10:59:25.505176+00:00 | 2024-01-08 10:59:25.505186+00:00 | 1 |
| 43 | p1co | Phenotype | all | True | pato | Phenotype And Trait Ontology | 2023-05-18 | http://purl.obolibrary.org/obo/pato/releases/2... | bd472f4971492109493d4ad8a779a8dd | https://github.com/pato-ontology/pato | 2024-01-08 10:59:25.505277+00:00 | 2024-01-08 10:59:25.505286+00:00 | 1 |
When instantiating a Bionty object, we can choose a source or version:
bionty_source = lb.BiontySource.filter(
source="hp", version="2023-06-17", organism="human"
).one()
phenotype_bt = lb.Phenotype.bionty(bionty_source=bionty_source)
phenotype_bt
Phenotype
Organism: human
Source: hp, 2023-06-17
#terms: 17653
📖 Phenotype.df(): ontology reference table
🔎 Phenotype.lookup(): autocompletion of terms
🎯 Phenotype.search(): free text search of terms
✅ Phenotype.validate(): strictly validate values
🧐 Phenotype.inspect(): full inspection of values
👽 Phenotype.standardize(): convert to standardized names
🪜 Phenotype.diff(): difference between two versions
🔗 Phenotype.ontology: Pronto.Ontology object
The currently used ontologies can be displayed using:
lb.BiontySource.filter(currently_used=True).df()
Show code cell output
| uid | entity | organism | currently_used | source | source_name | version | url | md5 | source_website | created_at | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||
| 1 | zvGR | Organism | vertebrates | True | ensembl | Ensembl | release-110 | https://ftp.ensembl.org/pub/release-110/specie... | f3faf95648d3a2b50fd3625456739706 | https://www.ensembl.org | 2024-01-08 10:59:25.500915+00:00 | 2024-01-08 10:59:25.500947+00:00 | 1 |
| 4 | TE9h | Organism | bacteria | True | ensembl | Ensembl | release-57 | https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... | ee28510ed5586ea7ab4495717c96efc8 | https://www.ensembl.org | 2024-01-08 10:59:25.501337+00:00 | 2024-01-08 10:59:25.501346+00:00 | 1 |
| 5 | OZIG | Organism | fungi | True | ensembl | Ensembl | release-57 | http://ftp.ensemblgenomes.org/pub/fungi/releas... | dbcde58f4396ab8b2480f7fe9f83df8a | https://www.ensembl.org | 2024-01-08 10:59:25.501438+00:00 | 2024-01-08 10:59:25.501447+00:00 | 1 |
| 6 | W07m | Organism | metazoa | True | ensembl | Ensembl | release-57 | http://ftp.ensemblgenomes.org/pub/metazoa/rele... | 424636a574fec078a61cbdddb05f9132 | https://www.ensembl.org | 2024-01-08 10:59:25.501538+00:00 | 2024-01-08 10:59:25.501548+00:00 | 1 |
| 7 | AVh3 | Organism | plants | True | ensembl | Ensembl | release-57 | https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... | eadaa1f3e527e4c3940c90c7fa5c8bf4 | https://www.ensembl.org | 2024-01-08 10:59:25.501638+00:00 | 2024-01-08 10:59:25.501647+00:00 | 1 |
| 8 | MdBu | Organism | all | True | ncbitaxon | NCBItaxon Ontology | 2023-06-20 | s3://bionty-assets/df_all__ncbitaxon__2023-06-... | 00d97ba65627f1cd65636d2df22ea76c | https://github.com/obophenotype/ncbitaxon | 2024-01-08 10:59:25.501739+00:00 | 2024-01-08 10:59:25.501749+00:00 | 1 |
| 9 | o36k | Gene | human | True | ensembl | Ensembl | release-110 | s3://bionty-assets/df_human__ensembl__release-... | 832f3947e83664588d419608a469b528 | https://www.ensembl.org | 2024-01-08 10:59:25.501843+00:00 | 2024-01-08 10:59:25.501853+00:00 | 1 |
| 11 | VTEw | Gene | mouse | True | ensembl | Ensembl | release-110 | s3://bionty-assets/df_mouse__ensembl__release-... | fa4ce130f2929aefd7ac3bc8eaf0c4de | https://www.ensembl.org | 2024-01-08 10:59:25.502049+00:00 | 2024-01-08 10:59:25.502059+00:00 | 1 |
| 13 | Uhnp | Gene | saccharomyces cerevisiae | True | ensembl | Ensembl | release-110 | s3://bionty-assets/df_saccharomyces cerevisiae... | 2e59495a3e87ea6575e408697dd73459 | https://www.ensembl.org | 2024-01-08 10:59:25.502254+00:00 | 2024-01-08 10:59:25.502263+00:00 | 1 |
| 14 | 000Q | Protein | human | True | uniprot | Uniprot | 2023-03 | s3://bionty-assets/df_human__uniprot__2023-03_... | 1c46e85c6faf5eff3de5b4e1e4edc4d3 | https://www.uniprot.org | 2024-01-08 10:59:25.502354+00:00 | 2024-01-08 10:59:25.502363+00:00 | 1 |
| 16 | tD7O | Protein | mouse | True | uniprot | Uniprot | 2023-03 | s3://bionty-assets/df_mouse__uniprot__2023-03_... | 9d5e9a8225011d3218e10f9bbb96a46c | https://www.uniprot.org | 2024-01-08 10:59:25.502558+00:00 | 2024-01-08 10:59:25.502567+00:00 | 1 |
| 18 | vqWI | CellMarker | human | True | cellmarker | CellMarker | 2.0 | s3://bionty-assets/human_cellmarker_2.0_CellMa... | d565d4a542a5c7e7a06255975358e4f4 | http://bio-bigdata.hrbmu.edu.cn/CellMarker | 2024-01-08 10:59:25.502762+00:00 | 2024-01-08 10:59:25.502771+00:00 | 1 |
| 19 | ypPK | CellMarker | mouse | True | cellmarker | CellMarker | 2.0 | s3://bionty-assets/mouse_cellmarker_2.0_CellMa... | 189586732c63be949e40dfa6a3636105 | http://bio-bigdata.hrbmu.edu.cn/CellMarker | 2024-01-08 10:59:25.502862+00:00 | 2024-01-08 10:59:25.502871+00:00 | 1 |
| 20 | 2Zjk | CellLine | all | True | clo | Cell Line Ontology | 2022-03-21 | https://data.bioontology.org/ontologies/CLO/su... | ea58a1010b7e745702a8397a526b3a33 | https://bioportal.bioontology.org/ontologies/CLO | 2024-01-08 10:59:25.502962+00:00 | 2024-01-08 10:59:25.502971+00:00 | 1 |
| 21 | 4shh | CellType | all | True | cl | Cell Ontology | 2023-08-24 | http://purl.obolibrary.org/obo/cl/releases/202... | 46e7dd89421f1255cf0191eca1548f73 | https://obophenotype.github.io/cell-ontology | 2024-01-08 10:59:25.503063+00:00 | 2024-01-08 10:59:25.503072+00:00 | 1 |
| 25 | LmWQ | Tissue | all | True | uberon | Uberon multi-species anatomy ontology | 2023-09-05 | http://purl.obolibrary.org/obo/uberon/releases... | abcee3ede566d1311d758b853ccdf5aa | http://obophenotype.github.io/uberon | 2024-01-08 10:59:25.503464+00:00 | 2024-01-08 10:59:25.503473+00:00 | 1 |
| 29 | zMWv | Disease | all | True | mondo | Mondo Disease Ontology | 2023-08-02 | http://purl.obolibrary.org/obo/mondo/releases/... | 7f33767422042eec29f08b501fc851db | https://mondo.monarchinitiative.org | 2024-01-08 10:59:25.503860+00:00 | 2024-01-08 10:59:25.503869+00:00 | 1 |
| 33 | cxPr | Disease | human | True | doid | Human Disease Ontology | 2023-03-31 | http://purl.obolibrary.org/obo/doid/releases/2... | 64f083a1e47867c307c8eae308afc3bb | https://disease-ontology.org | 2024-01-08 10:59:25.504256+00:00 | 2024-01-08 10:59:25.504265+00:00 | 1 |
| 35 | 2wto | ExperimentalFactor | all | True | efo | The Experimental Factor Ontology | 3.57.0 | http://www.ebi.ac.uk/efo/releases/v3.57.0/efo.owl | 2ecafc69b3aba7bdb31ad99438505c05 | https://bioportal.bioontology.org/ontologies/EFO | 2024-01-08 10:59:25.504455+00:00 | 2024-01-08 10:59:25.504464+00:00 | 1 |
| 37 | 3SSF | Phenotype | human | True | hp | Human Phenotype Ontology | 2023-06-17 | https://github.com/obophenotype/human-phenotyp... | 65e8d96bc81deb893163927063b10c06 | https://hpo.jax.org | 2024-01-08 10:59:25.504655+00:00 | 2024-01-08 10:59:25.504664+00:00 | 1 |
| 40 | nwdt | Phenotype | mammalian | True | mp | Mammalian Phenotype Ontology | 2023-05-31 | https://github.com/mgijax/mammalian-phenotype-... | be89052cf6d9c0b6197038fe347ef293 | https://github.com/mgijax/mammalian-phenotype-... | 2024-01-08 10:59:25.504955+00:00 | 2024-01-08 10:59:25.504964+00:00 | 1 |
| 41 | zAfB | Phenotype | zebrafish | True | zp | Zebrafish Phenotype Ontology | 2022-12-17 | https://github.com/obophenotype/zebrafish-phen... | 03430b567bf153216c0fa4c3440b3b24 | https://github.com/obophenotype/zebrafish-phen... | 2024-01-08 10:59:25.505071+00:00 | 2024-01-08 10:59:25.505083+00:00 | 1 |
| 43 | p1co | Phenotype | all | True | pato | Phenotype And Trait Ontology | 2023-05-18 | http://purl.obolibrary.org/obo/pato/releases/2... | bd472f4971492109493d4ad8a779a8dd | https://github.com/pato-ontology/pato | 2024-01-08 10:59:25.505277+00:00 | 2024-01-08 10:59:25.505286+00:00 | 1 |
| 44 | h0rU | Pathway | all | True | go | Gene Ontology | 2023-05-10 | https://data.bioontology.org/ontologies/GO/sub... | e9845499eadaef2418f464cd7e9ac92e | http://geneontology.org | 2024-01-08 10:59:25.505378+00:00 | 2024-01-08 10:59:25.505387+00:00 | 1 |
| 46 | fxHJ | BFXPipeline | all | True | lamin | Bioinformatics Pipeline | 1.0.0 | s3://bionty-assets/bfxpipelines.json | a7eff57a256994692fba46e0199ffc94 | https://lamin.ai | 2024-01-08 10:59:25.505587+00:00 | 2024-01-08 10:59:25.505596+00:00 | 1 |
| 47 | chfO | Drug | all | True | dron | Drug Ontology | 2023-03-10 | https://data.bioontology.org/ontologies/DRON/s... | 75e86011158fae76bb46d96662a33ba3 | https://bioportal.bioontology.org/ontologies/DRON | 2024-01-08 10:59:25.505686+00:00 | 2024-01-08 10:59:25.505695+00:00 | 1 |
| 48 | 7JhT | DevelopmentalStage | human | True | hsapdv | Human Developmental Stages | 2020-03-10 | http://aber-owl.net/media/ontologies/HSAPDV/11... | 52181d59df84578ed69214a5cb614036 | https://github.com/obophenotype/developmental-... | 2024-01-08 10:59:25.505786+00:00 | 2024-01-08 10:59:25.505795+00:00 | 1 |
| 49 | JIKv | DevelopmentalStage | mouse | True | mmusdv | Mouse Developmental Stages | 2020-03-10 | http://aber-owl.net/media/ontologies/MMUSDV/9/... | 5bef72395d853c7f65450e6c2a1fc653 | https://github.com/obophenotype/developmental-... | 2024-01-08 10:59:25.505886+00:00 | 2024-01-08 10:59:25.505895+00:00 | 1 |
| 50 | clid | Ethnicity | human | True | hancestro | Human Ancestry Ontology | 3.0 | https://github.com/EBISPOT/hancestro/raw/3.0/h... | 76dd9efda9c2abd4bc32fc57c0b755dd | https://github.com/EBISPOT/hancestro | 2024-01-08 10:59:25.505985+00:00 | 2024-01-08 10:59:25.505994+00:00 | 1 |
| 51 | rsbG | BioSample | all | True | ncbi | NCBI BioSample attributes | 2023-09 | s3://bionty-assets/df_all__ncbi__2023-09__BioS... | 918db9bd1734b97c596c67d9654a4126 | https://www.ncbi.nlm.nih.gov/biosample/docs/at... | 2024-01-08 10:59:25.506084+00:00 | 2024-01-08 10:59:25.506093+00:00 | 1 |
Show code cell content
!lamin delete --force test-phenotype
!rm -r test-phenotype
💡 deleting instance testuser1/test-phenotype
✅ deleted instance settings file: /home/runner/.lamin/instance--testuser1--test-phenotype.env
✅ instance cache deleted
✅ deleted '.lndb' sqlite file
❗ consider manually deleting your stored data: /home/runner/work/lamin-usecases/lamin-usecases/docs/test-phenotype